Zinc in PDB 7fse: Crystal Structure of T. Maritima Reverse Gyrase with A Minimal Latch

All present enzymatic activity of Crystal Structure of T. Maritima Reverse Gyrase with A Minimal Latch:
3.6.4.12; 5.6.2.2;

The structure of Crystal Structure of T. Maritima Reverse Gyrase with A Minimal Latch, PDB code: 7fse was solved by R.Rasche, D.Kummel, M.G.Rudolph, D.Klostermeier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.62 / 2.89
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	91.832, 91.832, 323.312, 90, 90, 90
R / Rfree (%)	21.3 / 26.4

The structure of Crystal Structure of T. Maritima Reverse Gyrase with A Minimal Latch also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of T. Maritima Reverse Gyrase with A Minimal Latch (pdb code 7fse). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of T. Maritima Reverse Gyrase with A Minimal Latch, PDB code: 7fse:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of T. Maritima Reverse Gyrase with A Minimal Latch


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of T. Maritima Reverse Gyrase with A Minimal Latch within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:58.7 occ:1.00 SG A:CYS14 2.3 52.4 1.0 SG A:CYS32 2.3 48.5 1.0 SG A:CYS11 2.3 41.3 1.0 SG A:CYS29 2.3 49.7 1.0 CB A:CYS14 3.1 47.2 1.0 CB A:CYS11 3.4 41.5 1.0 CB A:CYS32 3.6 42.8 1.0 CB A:CYS29 3.6 56.0 1.0 N A:CYS14 3.7 53.4 1.0 N A:CYS29 3.9 47.6 1.0 CA A:CYS14 4.0 41.9 1.0 N A:CYS32 4.2 51.7 1.0 CA A:CYS29 4.3 56.9 1.0 CA A:CYS32 4.5 43.3 1.0 CB A:PRO28 4.7 52.4 1.0 C A:CYS14 4.7 41.6 1.0 CA A:CYS11 4.8 42.9 1.0 C A:ASN13 4.8 47.8 1.0 C A:CYS29 4.9 53.2 1.0 N A:GLY15 4.9 47.4 1.0 O A:CYS29 4.9 42.6 1.0 N A:GLY16 4.9 46.8 1.0 ND2 A:ASN13 5.0 42.7 1.0 C A:PRO28 5.0 47.8 1.0 CB A:ASN13 5.0 42.0 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of T. Maritima Reverse Gyrase with A Minimal Latch


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of T. Maritima Reverse Gyrase with A Minimal Latch within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1102 b:74.0 occ:1.00 SG A:CYS577 2.3 66.1 1.0 SG A:CYS563 2.3 63.5 1.0 SG A:CYS574 2.3 76.5 1.0 SG A:CYS560 2.3 65.4 1.0 CB A:CYS574 3.0 56.0 1.0 CB A:CYS560 3.1 40.3 1.0 CB A:CYS577 3.4 79.8 1.0 CB A:CYS563 3.5 62.8 1.0 N A:CYS563 3.9 61.2 1.0 N A:CYS577 4.0 64.5 1.0 CA A:CYS563 4.2 67.6 1.0 CA A:CYS577 4.2 69.6 1.0 CA A:CYS574 4.5 62.3 1.0 CA A:CYS560 4.6 47.3 1.0 N A:GLY564 4.7 59.7 1.0 CB A:SER579 4.7 64.9 1.0 C A:CYS563 4.7 59.5 1.0 C A:CYS577 4.8 52.9 1.0 CB A:TYR565 4.8 46.0 1.0 N A:TYR565 4.8 54.4 1.0 N A:SER578 4.9 66.7 1.0 N A:SER579 4.9 58.8 1.0 C A:VAL576 5.0 61.7 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of T. Maritima Reverse Gyrase with A Minimal Latch


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of T. Maritima Reverse Gyrase with A Minimal Latch within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1103 b:76.9 occ:1.00 OE2 A:GLU303 2.2 71.2 1.0 OE1 A:GLU306 2.2 57.1 1.0 CD A:GLU303 3.1 73.4 1.0 CD A:GLU306 3.1 62.1 1.0 OE2 A:GLU306 3.4 77.0 1.0 OE1 A:GLU303 3.4 81.4 1.0 CG A:GLU303 4.4 65.4 1.0 CG1 A:VAL302 4.5 49.4 1.0 CG A:GLU306 4.5 50.4 1.0 CA A:GLU303 4.8 59.3 1.0 CB A:GLU306 5.0 50.2 1.0

V.Mhaindarkar, R.Rasche, D.Kummel, M.G.Rudolph, D.Klostermeier. Structure of Reverse Gyrase with A Minimal Latch That Supports Atp-Dependent Positive Supercoiling Without Specific Interactions with the Topoisomerase Domain Acta Crystallogr.,Sect.D 2023.
ISSN: ESSN 1399-0047
DOI: 10.1107/S2059798323002565